Browse Articles

  • Letter |

    This study tracks emergent ciprofloxacin-resistant Shigella sonnei in Vietnam, showing displacement of sensitive strains by others that acquired beta-lactam-antibiotic-resistance plasmids from commensal E. coli in infected individuals.

    • Pham Thanh Duy
    • , To Nguyen Thi Nguyen
    • , Duong Vu Thuy
    • , Hao Chung The
    • , Felicity Alcock
    • , Christine Boinett
    • , Ho Ngoc Dan Thanh
    • , Ha Thanh Tuyen
    • , Guy E. Thwaites
    • , Maia A. Rabaa
    •  & Stephen Baker
  • Article |

    Inflammatory bowel diseases (IBD) are associated with increased faecal N-acylethanolamines (NAEs), which are primarily host-produced signalling lipids, in patients and a mouse model of colitis. These metabolites can enhance the growth of bacterial species enriched in IBD faecal samples and are associated with the expression of respiratory chain genes necessary for microbial metabolism of NAEs.

    • Nadine Fornelos
    • , Eric A. Franzosa
    • , Jason Bishai
    • , John W. Annand
    • , Akihiko Oka
    • , Jason Lloyd-Price
    • , Timothy D. Arthur
    • , Ashley Garner
    • , Julian Avila-Pacheco
    • , Henry J. Haiser
    • , Andrew C. Tolonen
    • , Jeffrey A. Porter
    • , Clary B. Clish
    • , R. Balfour Sartor
    • , Curtis Huttenhower
    • , Hera Vlamakis
    •  & Ramnik J. Xavier
  • Letter |

    The autophagy proteins Beclin 1 and FIP200, but not other essential autophagy components, such as ATG5, ATG16L1 or ATG7, regulate quiescence of tissue-resident macrophages, thereby modulating immune activation and resistance to Listeria monocytogenes infection.

    • Ya-Ting Wang
    • , Konstantin Zaitsev
    • , Qun Lu
    • , Shan Li
    • , W. Timothy Schaiff
    • , Ki-Wook Kim
    • , Lindsay Droit
    • , Craig B. Wilen
    • , Chandni Desai
    • , Dale R. Balce
    • , Robert C. Orchard
    • , Anthony Orvedahl
    • , Sunmin Park
    • , Darren Kreamalmeyer
    • , Scott A. Handley
    • , John D. Pfeifer
    • , Megan T. Baldridge
    • , Maxim N. Artyomov
    • , Christina L. Stallings
    •  & Herbert W. Virgin
  • Article |

    Co-housing mice is shown to induce resistance against enterobacterial infection after antibiotic treatment through the ability to retain or share Klebsiella michiganensis, which is necessary and sufficient to prevent infection through competition for nutrients.

    • Rita A. Oliveira
    • , Katharine M. Ng
    • , Margarida B. Correia
    • , Vitor Cabral
    • , Handuo Shi
    • , Justin L. Sonnenburg
    • , Kerwyn Casey Huang
    •  & Karina B. Xavier
  • Article |

    The PLate Coverage Algorithm (PLCA) determines the culture plates required for culture-enriched metagenomics and enables the recovery of greater taxonomic diversity, better quality metagenome-assembled genomes and improved functional annotations compared to metagenomics alone, indicating its utility for other microbiomes, especially those dominated by host DNA.

    • Fiona J. Whelan
    • , Barbara Waddell
    • , Saad A. Syed
    • , Shahrokh Shekarriz
    • , Harvey R. Rabin
    • , Michael D. Parkins
    •  & Michael G. Surette
  • Letter |

    In an interesting demonstration of how bacterial subcellular organization influences physiology, polar accumulation of PopZ protein in a membraneless microdomain is found to drive asymmetric phosphorylation of CtrA-P, which creates a gradient that is responsible for asymmetric cell division in Caulobacter.

    • Keren Lasker
    • , Lexy von Diezmann
    • , Xiaofeng Zhou
    • , Daniel G. Ahrens
    • , Thomas H. Mann
    • , W. E. Moerner
    •  & Lucy Shapiro
  • Article |

    This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.

    • Xianding Deng
    • , Asmeeta Achari
    • , Scot Federman
    • , Guixia Yu
    • , Sneha Somasekar
    • , Inês Bártolo
    • , Shigeo Yagi
    • , Placide Mbala-Kingebeni
    • , Jimmy Kapetshi
    • , Steve Ahuka-Mundeke
    • , Jean-Jacques Muyembe-Tamfum
    • , Asim A. Ahmed
    • , Vijay Ganesh
    • , Manasi Tamhankar
    • , Jean L. Patterson
    • , Nicaise Ndembi
    • , Dora Mbanya
    • , Lazare Kaptue
    • , Carole McArthur
    • , José E. Muñoz-Medina
    • , Cesar R. Gonzalez-Bonilla
    • , Susana López
    • , Carlos F. Arias
    • , Shaun Arevalo
    • , Steve Miller
    • , Mars Stone
    • , Michael Busch
    • , Kristina Hsieh
    • , Sharon Messenger
    • , Debra A. Wadford
    • , Mary Rodgers
    • , Gavin Cloherty
    • , Nuno R. Faria
    • , Julien Thézé
    • , Oliver G. Pybus
    • , Zoraima Neto
    • , Joana Morais
    • , Nuno Taveira
    • , John R. Hackett Jr.
    •  & Charles Y. Chiu
  • Letter |

    Bacterial cell wall amidases typically hydrolyse crosslinked peptidoglycan between daughter cells so they can separate. An amidase that cleaves uncrosslinked peptidoglycan and its regulator are identified here and shown to regulate cell growth, rather than separation. This enzyme regulates the density of peptidoglycan assembly sites, ensuring coordination between cell expansion and cell division.

    • Truc Do
    • , Kaitlin Schaefer
    • , Ace George Santiago
    • , Kathryn A. Coe
    • , Pedro B. Fernandes
    • , Daniel Kahne
    • , Mariana G. Pinho
    •  & Suzanne Walker
  • Article |

    Commensal-colonization-factor-producing Bacteroidetes protect against Klebsiella pneumoniae colonization and infection in the gut via IL-36 signalling and macrophages, and these commensals can limit transmission between hosts, whereas Proteobacteria are important for colonization resistance in the upper airway.

    • Richard P. Sequeira
    • , Julie A. K. McDonald
    • , Julian R. Marchesi
    •  & Thomas B. Clarke
  • Article |

    The lipopolysaccharide of the intracellular pathogen Shigella, in particular its O antigen, interacts with caspases and blocks their activation to prevent apoptosis.

    • Saskia D. Günther
    • , Melanie Fritsch
    • , Jens M. Seeger
    • , Lars M. Schiffmann
    • , Scott J. Snipas
    • , Maria Coutelle
    • , Thomas A. Kufer
    • , Paul G. Higgins
    • , Veit Hornung
    • , Maria L. Bernardini
    • , Stefan Höning
    • , Martin Krönke
    • , Guy S. Salvesen
    •  & Hamid Kashkar
  • Letter |

    Quantitative stable isotope probing and gene expression analyses in anoxic Namibian shelf sediments reveal that representatives of the Asgard candidate phylum Candidatus Lokiarchaeota are capable of homoacetogenesis, a metabolic strategy of high energetic efficiency that may explain how these archaea thrive in the energy-limited seafloor subsurface environment.

    • William D. Orsi
    • , Aurèle Vuillemin
    • , Paula Rodriguez
    • , Ömer K. Coskun
    • , Gonzalo V. Gomez-Saez
    • , Gaute Lavik
    • , Volker Mohrholz
    •  & Timothy G. Ferdelman
  • Article |

    Galacturonic acid produced by Bacteroides thetaiotamicron is shown to be sensed by enterohaemorrhagic Escherichia coli and Citrobacter rodentium to initiate an infection program that includes its use as a carbon source and regulation of the type III secretion system, leading to colitis and inflammation.

    • Angel G. Jimenez
    • , Melissa Ellermann
    • , Wade Abbott
    •  & Vanessa Sperandio
  • News & Views |

    The host protein cyclophilin A binds to the HIV-1 capsid and its role in infection has long been enigmatic. A new study shows that this interaction protects the virus from inhibition by TRIM5α in physiologically relevant primary human cells.

    • Christopher Aiken
  • Comment |

    As microbiome science expands, academic centres scramble to fill many needs, from service provider to industry liaison. A newly created network aims to share strategies and accelerate knowledge transfer, and invites others to join the efforts.

    • Jennifer B. H. Martiny
    • , Katrine L. Whiteson
    • , Brendan J. M. Bohannan
    • , Lawrence A. David
    • , Nicole A. Hynson
    • , Margaret McFall-Ngai
    • , John F. Rawls
    • , Thomas M. Schmidt
    • , Zaid Abdo
    • , Martin J. Blaser
    • , Seth Bordenstein
    • , Christian Bréchot
    • , Carolee T. Bull
    • , Pieter Dorrestein
    • , Jonathan A. Eisen
    • , Ferran Garcia-Pichel
    • , Jack Gilbert
    • , Kirsten S. Hofmockel
    • , Mary L. Holtz
    • , Rob Knight
    • , David B. Mark Welch
    • , Daniel McDonald
    • , Barbara Methé
    • , Nigel J. Mouncey
    • , Noel T. Mueller
    • , Catherine A. Pfister
    • , Lita Proctor
    •  & Joel L. Sachs
  • News & Views |

    Two recent studies reveal a virus anti-defence strategy whereby large, ‘jumbo’ phages protect themselves from both restriction endonucleases and DNA-targeting CRISPR–Cas systems, but not from RNA-targeting ones, by encapsulating the phage genome inside the cell in a ‘nucleus’-like shell that is impenetrable for CRISPR effectors.

    • Eugene V. Koonin
    •  & Mart Krupovic
  • News & Views |

    Metabolic adaptation plays a key role in determining the composition of microbial ecosystems. A new study shows that in the inflamed gut, pathogenic Enterobacteriaceae can reprogramme their metabolism towards diet-derived l-serine utilization to outcompete the resident microbiota and cause disease.

    • Woongjae Yoo
    •  & Mariana X. Byndloss
  • News & Views |

    Baloxavir marboxil (BXM) represents a promising advance in antiviral chemotherapies for influenza infections. Identification of transmissible BXM-resistant strains in Japan may hit pause on widespread adoption of this therapy and could lead to revision of surveillance practices for emerging viruses.

    • Karen A. Kormuth
    •  & Seema S. Lakdawala
  • News & Views |

    Adding a flap on the top of an insecticide-treated bednet helps to intercept blood-seeking mosquitoes and allows a wider range of insecticides to be used together. Net buyers must now make a challenging decision for each target area: which net product will be most cost-effective, given the resistance in local vectors?

    • Jo Lines
  • Editorial |

    Nature Microbiology will offer authors the option of publishing a peer-review file that includes anonymous peer-review reports, author responses and our decision letters. We will also request that articles include more source data and are more transparent in reporting data availability.

  • Article
    | Open Access

    Shotgun metagenomic sequencing (using the MinION platform) of mock microbial communities and faecal samples from healthy and ill preterm infants can be used to identify pathogens and their antimicrobial resistance gene profiles in real time, indicating the potential for translation into clinical settings.

    • Richard M. Leggett
    • , Cristina Alcon-Giner
    • , Darren Heavens
    • , Shabhonam Caim
    • , Thomas C. Brook
    • , Magdalena Kujawska
    • , Samuel Martin
    • , Ned Peel
    • , Holly Acford-Palmer
    • , Lesley Hoyles
    • , Paul Clarke
    • , Lindsay J. Hall
    •  & Matthew D. Clark
  • Article |

    Herpesviruses are shown to specifically block innate antiviral responses by inducing the aggregation of key signalling molecules nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) essential modulator (NEMO) and receptor-interacting protein kinase 1 (RIPK1) and their degradation by selective autophagy, thereby blocking the activation of NF-κB and the induction of necroptosis, respectively.

    • Elena Muscolino
    • , Rebekka Schmitz
    • , Stefan Loroch
    • , Enrico Caragliano
    • , Carola Schneider
    • , Matteo Rizzato
    • , Young-Hyun Kim
    • , Eva Krause
    • , Vanda Juranić Lisnić
    • , Albert Sickmann
    • , Rudolph Reimer
    • , Eleonore Ostermann
    •  & Wolfram Brune
  • Article |

    The comparison of the ability of native and engineered gene clusters transferred into bacteria that live on or inside cereal roots to regulate nitrogenase activity reveals different strategies to control nitrogen fixation in rhizobia and paves the way to engineer a bacterium able to deliver high nitrogen fluxes to crops.

    • Min-Hyung Ryu
    • , Jing Zhang
    • , Tyler Toth
    • , Devanshi Khokhani
    • , Barney A. Geddes
    • , Florence Mus
    • , Amaya Garcia-Costas
    • , John W. Peters
    • , Philip S. Poole
    • , Jean-Michel Ané
    •  & Christopher A. Voigt
  • Article |

    The structure of the FlaG–FlaF complexes from Sulfolobus acidocaldarius, combined with mutational and biochemical studies, suggests that these proteins form a heterotetrameric complex in which FlaF regulates the filamentation of FlaG and anchoring of the archaellum to the S-layer, thereby modulating motility.

    • Chi-Lin Tsai
    • , Patrick Tripp
    • , Shamphavi Sivabalasarma
    • , Changyi Zhang
    • , Marta Rodriguez-Franco
    • , Rebecca L. Wipfler
    • , Paushali Chaudhury
    • , Ankan Banerjee
    • , Morgan Beeby
    • , Rachel J. Whitaker
    • , John A. Tainer
    •  & Sonja-Verena Albers
  • Letter |

    Metagenomic sequencing of near-surface marine viral communities sampled monthly over 5 years revealed that overall communities were stable over time, although minor population variants were more variable, which is consistent with Red Queen-like dynamics.

    • J. Cesar Ignacio-Espinoza
    • , Nathan A. Ahlgren
    •  & Jed A. Fuhrman
  • Letter |

    This study reports that flavivirus transmission by mosquitoes to mice is increased if mosquitoes feed subsequently on non-infectious blood, possibly because feeding causes microperforations in the gut. Modelling shows this could explain how A. aegypti can sustain an explosive epidemic such as Zika virus despite its perceived poor vector competence.

    • Philip M. Armstrong
    • , Hanna Y. Ehrlich
    • , Tereza Magalhaes
    • , Megan R. Miller
    • , Patrick J. Conway
    • , Angela Bransfield
    • , Michael J. Misencik
    • , Andrea Gloria-Soria
    • , Joshua L. Warren
    • , Theodore G. Andreadis
    • , John J. Shepard
    • , Brian D. Foy
    • , Virginia E. Pitzer
    •  & Doug E. Brackney
  • Letter |

    This paper identifies a Serratia jumbo phage that, on infection, leads to the formation of a nucleus-like structure that protects phage DNA from CRISPR–Cas defence systems. However, the phage is still susceptible to CRISPR–Cas RNA targeting in the cytoplasm.

    • Lucia M. Malone
    • , Suzanne L. Warring
    • , Simon A. Jackson
    • , Carolin Warnecke
    • , Paul P. Gardner
    • , Laura F. Gumy
    •  & Peter C. Fineran
  • Brief Communication |

    Electron micrographs show that mouse and rat segmented filamentous bacterium (SFB) unicellular intracellular offspring (IO) are flagellated and that flagellation occurs before IO release from SFB filaments.

    • Iris Nkamba
    • , Céline Mulet
    • , Gyanendra P. Dubey
    • , Olivier Gorgette
    • , Aurélie Couesnon
    • , Audrey Salles
    • , Maryse Moya-Nilges
    • , Vincent Jung
    • , Valérie Gaboriau-Routhiau
    • , Ida Chiara Guerrera
    • , Tatsuichiro Shima
    • , Yoshinori Umesaki
    • , Giulia Nigro
    • , Jacomina Krijnse-Locker
    • , Marion Bérard
    • , Nadine Cerf-Bensussan
    • , Philippe J. Sansonetti
    •  & Pamela Schnupf
  • Letter |

    Reactive oxygen species produced by macrophages following infection with Staphylococcus aureus attack bacterial iron–sulfur cluster-containing proteins, thereby leading to alterations in bacterial metabolism that increase their tolerance to antibiotics.

    • Sarah E. Rowe
    • , Nikki J. Wagner
    • , Lupeng Li
    • , Jenna E. Beam
    • , Alec D. Wilkinson
    • , Lauren C. Radlinski
    • , Qing Zhang
    • , Edward A. Miao
    •  & Brian P. Conlon
  • Letter |

    This work reports an analysis of primary and secondary immune responses in ten women infected with ZIKV for 224 days following an acute symptomatic Zika virus infection. CD4+ T-cell responses broadly targeted the whole Zika genome, whereas CD8+ T cells were strongly biased towards non-structural proteins.

    • Pierre Tonnerre
    • , Juliana G. Melgaço
    • , Almudena Torres-Cornejo
    • , Marcelo A. Pinto
    • , Constanze Yue
    • , Johannes Blümel
    • , Paulo Sergio Fonseca de Sousa
    • , Vinicius da Motta de Mello
    • , Julio Moran
    • , Ana M. Bispo de Filippis
    • , David Wolski
    • , Alba Grifoni
    • , Alessandro Sette
    • , Dan H. Barouch
    • , Ruben C. Hoogeveen
    • , Sally A. Baylis
    • , Georg M. Lauer
    •  & Lia L. Lewis-Ximenez
  • Letter |

    The addition of a small net barrier above a standard bednet targets malaria vectors and—as these barriers are further distanced from sleepers—paves the way for the use of a wider range of insecticides to curtail malaria transmission.

    • Gregory P. D. Murray
    • , Natalie Lissenden
    • , Jeff Jones
    • , Vitaly Voloshin
    • , K. Hyacinthe Toé
    • , Ellie Sherrard-Smith
    • , Geraldine M. Foster
    • , Thomas S. Churcher
    • , Josephine E. A. Parker
    • , Catherine E. Towers
    • , Sagnon N’Falé
    • , Wamdaogo M. Guelbeogo
    • , Hilary Ranson
    • , David Towers
    •  & Philip J. McCall
  • Article |

    This study reports a microscopy-based screen to find microRNAs (miRNAs) that control infection by Salmonella and Shigella, showing they have different requirements. Two miRNAs decrease Shigella actin motility through N-WASP and one miRNA inhibits Salmonella by targeting TGS2, a regulator of phagolysosomal trafficking.

    • Carmen Aguilar
    • , Ana Rita Cruz
    • , Ines Rodrigues Lopes
    • , Claire Maudet
    • , Ushasree Sunkavalli
    • , Ricardo Jorge Silva
    • , Malvika Sharan
    • , Clivia Lisowski
    • , Sara Zaldívar-López
    • , Juan José Garrido
    • , Mauro Giacca
    • , Miguel Mano
    •  & Ana Eulalio
  • Brief Communication |

    Resistance to baloxavir marboxil, a recently approved drug to treat influenza infection, was thought to make the virus less fit. This study reports that resistant viruses isolated from Japanese patients have normal replicative abilities and pathogenicity in animal models and thus might spread in humans.

    • Masaki Imai
    • , Makoto Yamashita
    • , Yuko Sakai-Tagawa
    • , Kiyoko Iwatsuki-Horimoto
    • , Maki Kiso
    • , Jurika Murakami
    • , Atsuhiro Yasuhara
    • , Kosuke Takada
    • , Mutsumi Ito
    • , Noriko Nakajima
    • , Kenta Takahashi
    • , Tiago J. S. Lopes
    • , Jayeeta Dutta
    • , Zenab Khan
    • , Divya Kriti
    • , Harm van Bakel
    • , Akifumi Tokita
    • , Haruhisa Hagiwara
    • , Naomi Izumida
    • , Haruo Kuroki
    • , Tamon Nishino
    • , Noriyuki Wada
    • , Michiko Koga
    • , Eisuke Adachi
    • , Daisuke Jubishi
    • , Hideki Hasegawa
    •  & Yoshihiro Kawaoka
  • Letter |

    The gut microbiota enhances murine norovirus infection in distal regions of the gut, but inhibits viral infection in the proximal small intestine via altered bile acid metabolism and consequent type III interferon production.

    • Katrina R. Grau
    • , Shu Zhu
    • , Stefan T. Peterson
    • , Emily W. Helm
    • , Drake Philip
    • , Matthew Phillips
    • , Abel Hernandez
    • , Holly Turula
    • , Philip Frasse
    • , Vincent R. Graziano
    • , Craig B. Wilen
    • , Christiane E. Wobus
    • , Megan T. Baldridge
    •  & Stephanie M. Karst
  • Article |

    Single-cell sequencing of flagellated heterotrophic unicellular eukaryotes provides insights into the dynamics of mitochondrial genome evolution.

    • Jeremy G. Wideman
    • , Adam Monier
    • , Raquel Rodríguez-Martínez
    • , Guy Leonard
    • , Emily Cook
    • , Camille Poirier
    • , Finlay Maguire
    • , David S. Milner
    • , Nicholas A. T. Irwin
    • , Karen Moore
    • , Alyson E. Santoro
    • , Patrick J. Keeling
    • , Alexandra Z. Worden
    •  & Thomas A. Richards
  • Article |

    In this work, Fang et al. analyse the epigenetic landscape of Clostridioides difficile and identify a DNA methyltransferase present across C. difficile strains that is required for optimal sporulation and in vivo colonization and disease.

    • Pedro H. Oliveira
    • , John W. Ribis
    • , Elizabeth M. Garrett
    • , Dominika Trzilova
    • , Alex Kim
    • , Ognjen Sekulovic
    • , Edward A. Mead
    • , Theodore Pak
    • , Shijia Zhu
    • , Gintaras Deikus
    • , Marie Touchon
    • , Martha Lewis-Sandari
    • , Colleen Beckford
    • , Nathalie E. Zeitouni
    • , Deena R. Altman
    • , Elizabeth Webster
    • , Irina Oussenko
    • , Supinda Bunyavanich
    • , Aneel K. Aggarwal
    • , Ali Bashir
    • , Gopi Patel
    • , Frances Wallach
    • , Camille Hamula
    • , Shirish Huprikar
    • , Eric E. Schadt
    • , Robert Sebra
    • , Harm van Bakel
    • , Andrew Kasarskis
    • , Rita Tamayo
    • , Aimee Shen
    •  & Gang Fang
  • News & Views |

    Culture-independent methods capable of connecting bacteriophages (phages) to their target host bacteria will help define the roles of phages in host-associated microbiotas. A recent study used fluorescently dyed intestinal phages to identify novel phage–bacterial interactions from the human intestine.

    • Cydney N. Johnson
    •  & Breck A. Duerkop
  • News & Views |

    A newly discovered energy-linked carbonic anhydrase, DabBA2, is a two-protein complex responsible for inorganic carbon accumulation in the sulfur bacterium Halothiobacillus neapolitanus. DABs are present in a wide range of proteobacterial clades, suggesting that they function in diverse metabolic pathways.

    • G. Dean Price
    • , Benedict M. Long
    •  & Britta Förster
  • Editorial |

    It’s an exciting time to be a microbiologist and we have the honour and privilege of having front-row tickets to see the field develop and progress. As we take stock of the past year, we will count down the days until 2020 by celebrating the field and the season with a microbiology advent calendar.

  • News & Views |

    Influenza vaccine strain selection is informed by international efforts to track antigenic change, focusing on the viral hemagglutinin protein. Recent research advocates monitoring neuraminidase for immune escape mutations that could reduce vaccine efficacy.

    • Annette Fox
    •  & Louise Carolan
  • Letter |

    The in vivo structure of a T2SS from Legionella pneumophila elucidates the structure and function of the different components of this macromolecular complex that exports a wide range of virulence factors.

    • Debnath Ghosal
    • , Ki Woo Kim
    • , Huaixin Zheng
    • , Mohammed Kaplan
    • , Hilary K. Truchan
    • , Alberto E. Lopez
    • , Ian E. McIntire
    • , Joseph P. Vogel
    • , Nicholas P. Cianciotto
    •  & Grant J. Jensen
  • Letter |

    Hergenrother and colleagues develop a web portal to help predict key permeation aspects of query compounds using the eNTRy rules they recently developed. They use this approach to screen antibiotics that are effective against Gram-positive bacteria and engineer a modified version of a FabI inhibitor that is an effective Gram-negative antibiotic.

    • Erica N. Parker
    • , Bryon S. Drown
    • , Emily J. Geddes
    • , Hyang Yeon Lee
    • , Nahed Ismail
    • , Gee W. Lau
    •  & Paul J. Hergenrother
  • Article |

    The combined use of genome sequencing, cultivation and phenotypic characterization of 79 globally distributed strains from the bacterial phylum Planctomycetes sheds light on their varied cell shapes, modes of cell division and extensive signalling and metabolic potential.

    • Sandra Wiegand
    • , Mareike Jogler
    • , Christian Boedeker
    • , Daniela Pinto
    • , John Vollmers
    • , Elena Rivas-Marín
    • , Timo Kohn
    • , Stijn H. Peeters
    • , Anja Heuer
    • , Patrick Rast
    • , Sonja Oberbeckmann
    • , Boyke Bunk
    • , Olga Jeske
    • , Anke Meyerdierks
    • , Julia E. Storesund
    • , Nicolai Kallscheuer
    • , Sebastian Lücker
    • , Olga M. Lage
    • , Thomas Pohl
    • , Broder J. Merkel
    • , Peter Hornburger
    • , Ralph-Walter Müller
    • , Franz Brümmer
    • , Matthias Labrenz
    • , Alfred M. Spormann
    • , Huub J. M. Op den Camp
    • , Jörg Overmann
    • , Rudolf Amann
    • , Mike S. M. Jetten
    • , Thorsten Mascher
    • , Marnix H. Medema
    • , Damien P. Devos
    • , Anne-Kristin Kaster
    • , Lise Øvreås
    • , Manfred Rohde
    • , Michael Y. Galperin
    •  & Christian Jogler
  • Author Correction |

    • Linwei Wu
    • , Daliang Ning
    • , Bing Zhang
    • , Yong Li
    • , Ping Zhang
    • , Xiaoyu Shan
    • , Qiuting Zhang
    • , Mathew Robert Brown
    • , Zhenxin Li
    • , Joy D. Van Nostrand
    • , Fangqiong Ling
    • , Naijia Xiao
    • , Ya Zhang
    • , Julia Vierheilig
    • , George F. Wells
    • , Yunfeng Yang
    • , Ye Deng
    • , Qichao Tu
    • , Aijie Wang
    • , Dany Acevedo
    • , Miriam Agullo-Barcelo
    • , Pedro J. J. Alvarez
    • , Lisa Alvarez-Cohen
    • , Gary L. Andersen
    • , Juliana Calabria de Araujo
    • , Kevin F. Boehnke
    • , Philip Bond
    • , Charles B. Bott
    • , Patricia Bovio
    • , Rebecca K. Brewster
    • , Faizal Bux
    • , Angela Cabezas
    • , Léa Cabrol
    • , Si Chen
    • , Craig S. Criddle
    • , Ye Deng
    • , Claudia Etchebehere
    • , Amanda Ford
    • , Dominic Frigon
    • , Janeth Sanabria
    • , James S. Griffin
    • , April Z. Gu
    • , Moshe Habagil
    • , Lauren Hale
    • , Steven D. Hardeman
    • , Marc Harmon
    • , Harald Horn
    • , Zhiqiang Hu
    • , Shameem Jauffur
    • , David R. Johnson
    • , Jurg Keller
    • , Alexander Keucken
    • , Sheena Kumari
    • , Cintia Dutra Leal
    • , Laura A. Lebrun
    • , Jangho Lee
    • , Minjoo Lee
    • , Zarraz M. P. Lee
    • , Yong Li
    • , Zhenxin Li
    • , Mengyan Li
    • , Xu Li
    • , Fangqiong Ling
    • , Yu Liu
    • , Richard G. Luthy
    • , Leda C. Mendonça-Hagler
    • , Francisca Gleire Rodriguez de Menezes
    • , Arthur J. Meyers
    • , Amin Mohebbi
    • , Per H. Nielsen
    • , Daliang Ning
    • , Adrian Oehmen
    • , Andrew Palmer
    • , Prathap Parameswaran
    • , Joonhong Park
    • , Deborah Patsch
    • , Valeria Reginatto
    • , Francis L. de los Reyes III
    • , Bruce E. Rittmann
    • , Adalberto Noyola
    • , Simona Rossetti
    • , Xiaoyu Shan
    • , Jatinder Sidhu
    • , William T. Sloan
    • , Kylie Smith
    • , Oscarina Viana de Sousa
    • , David A. Stahl
    • , Kyle Stephens
    • , Renmao Tian
    • , James M. Tiedje
    • , Nicholas B. Tooker
    • , Qichao Tu
    • , Joy D. Van Nostrand
    • , Daniel De los Cobos Vasconcelos
    • , Julia Vierheilig
    • , Michael Wagner
    • , Steve Wakelin
    • , Aijie Wang
    • , Bei Wang
    • , Joseph E. Weaver
    • , George F. Wells
    • , Stephanie West
    • , Paul Wilmes
    • , Sung-Geun Woo
    • , Linwei Wu
    • , Jer-Horng Wu
    • , Liyou Wu
    • , Chuanwu Xi
    • , Naijia Xiao
    • , Meiying Xu
    • , Tao Yan
    • , Yunfeng Yang
    • , Min Yang
    • , Michelle Young
    • , Haowei Yue
    • , Bing Zhang
    • , Ping Zhang
    • , Qiuting Zhang
    • , Ya Zhang
    • , Tong Zhang
    • , Qian Zhang
    • , Wen Zhang
    • , Yu Zhang
    • , Hongde Zhou
    • , Jizhong Zhou
    • , Xianghua Wen
    • , Thomas P. Curtis
    • , Qiang He
    • , Zhili He
    • , Matthew Brown
    • , Tong Zhang
    • , Zhili He
    • , Jurg Keller
    • , Per H. Nielsen
    • , Pedro J. J. Alvarez
    • , Craig S. Criddle
    • , Michael Wagner
    • , James M. Tiedje
    • , Qiang He
    • , Thomas P. Curtis
    • , David A. Stahl
    • , Lisa Alvarez-Cohen
    • , Bruce E. Rittmann
    • , Xianghua Wen
    •  & Jizhong Zhou
  • Letter |

    A consortium of four human gut microbiota species, including Eggerthella lenta, can convert plant-derived lignans into bioactive enterolignans via a five-step pathway, providing mechanistic insight into the production of these protective metabolites.

    • Elizabeth N. Bess
    • , Jordan E. Bisanz
    • , Fauna Yarza
    • , Annamarie Bustion
    • , Barry E. Rich
    • , Xingnan Li
    • , Seiya Kitamura
    • , Emily Waligurski
    • , Qi Yan Ang
    • , Diana L. Alba
    • , Peter Spanogiannopoulos
    • , Stephen Nayfach
    • , Suneil K. Koliwad
    • , Dennis W. Wolan
    • , Adrian A. Franke
    •  & Peter J. Turnbaugh
  • Article |

    Members of the Enterobacteriaceae, including adherent invasive Escherichia coli, reprogram their metabolism to preferentially consume dietary serine during periods of inflammation in the gut to promote their growth and outcompete other microbiome members.

    • Sho Kitamoto
    • , Christopher J. Alteri
    • , Michael Rodrigues
    • , Hiroko Nagao-Kitamoto
    • , Kohei Sugihara
    • , Stephanie D. Himpsl
    • , Malak Bazzi
    • , Mao Miyoshi
    • , Tatsuki Nishioka
    • , Atsushi Hayashi
    • , Tina L. Morhardt
    • , Peter Kuffa
    • , Helmut Grasberger
    • , Mohamad El-Zaatari
    • , Shrinivas Bishu
    • , Chiharu Ishii
    • , Akiyoshi Hirayama
    • , Kathryn A. Eaton
    • , Belgin Dogan
    • , Kenneth W. Simpson
    • , Naohiro Inohara
    • , Harry L. T. Mobley
    • , John Y. Kao
    • , Shinji Fukuda
    • , Nicolas Barnich
    •  & Nobuhiko Kamada